/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb is in gromacs-data 2018.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 | ACE 1
3 4 HH3 CH3 C O
AIB 3
1 1 H N -C CA
3 4 HB1 CB1 CA N
3 4 HB2 CB2 CA N
ALA 3
1 1 H N -C CA
1 5 HA CA N C CB
3 4 HB CB CA N
ARG 8
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
2 6 HG CG CD CB
2 6 HD CD NE CG
1 1 HE NE CD CZ
2 3 HH1 NH1 CZ NE
2 3 HH2 NH2 CZ NE
ARGN 8
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
2 6 HG CG CD CB
2 6 HD CD NE CG
1 1 HE NE CD CZ
1 2 HH1 NH1 CZ NE
2 3 HH2 NH2 CZ NE
ASN 4
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
2 3 HD2 ND2 CG CB
ASP 3
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
ASPH 4
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
1 2 HD2 OD2 CG CB
CYS2 3
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB SG CA
CYSH 4
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB SG CA
1 2 HG SG CB CA
GLN 5
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
2 6 HG CG CD CB
2 3 HE2 NE2 CD CG
QLN 6
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
2 6 HG CG CD CB
2 3 HE2 NE2 CD CG
1 3 HE1 OE1 CD CG
GLU 4
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
2 6 HG CG CD CB
PGLU 4
1 1 H N CD CA
1 5 HA CA N C CB
2 6 HB CB CG CA
2 6 HG CG CD CB
GLUH 5
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
2 6 HG CG CD CB
1 2 HE2 OE2 CD CG
GLY 2
1 1 H N -C CA
2 6 HA CA C N
HISD 6
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
1 1 HD2 CD2 CG NE2
1 1 HE1 CE1 ND1 NE2
1 1 HD1 ND1 CG CE1
HISE 6
1 1 H N -C CA
2 6 HB CB CG CA
1 5 HA CA N C CB
1 1 HE2 NE2 CE1 CD2
1 1 HD2 CD2 CG NE2
1 1 HE1 CE1 ND1 NE2
HISH 7
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
1 1 HD2 CD2 CG NE2
1 1 HE1 CE1 ND1 NE2
1 1 HD1 ND1 CG CE1
1 1 HE2 NE2 CE1 CD2
HO4 1
3 10 HW OW
HO5 1
4 11 HW OW
HOH 1
2 7 HW OW
ILE 6
1 1 H N -C CA
1 5 HA CA N C CB
1 5 HB CB CA CG1 CG2
2 6 HG1 CG1 CD CB
3 4 HG2 CG2 CB CA
3 4 HD CD CG1 CB
LEU 6
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
1 5 HG CG CB CD1 CD2
3 4 HD1 CD1 CG CB
3 4 HD2 CD2 CG CB
LYS 7
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
2 6 HG CG CD CB
2 6 HD CD CE CG
2 6 HE CE NZ CD
2 4 HZ NZ CE CD
LYSH 7
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
2 6 HG CG CD CB
2 6 HD CD CE CG
2 6 HE CE NZ CD
3 4 HZ NZ CE CD
MET 5
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
2 6 HG CG SD CB
3 4 HE CE SD CG
NAC 2
1 1 H N -C CH3
3 4 HH3 CH3 N -C
NH2 1
2 3 H N -C -CA
NHE 1
2 3 H N -C -CA
PHE 8
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
1 1 HD1 CD1 CG CE1
1 1 HD2 CD2 CG CE2
1 1 HE1 CE1 CD1 CZ
1 1 HE2 CE2 CD2 CZ
1 1 HZ CZ CE1 CE2
PRO 4
1 5 HA CA N C CB
2 6 HB CB CG CA
2 6 HG CG CD CB
2 6 HD CD N CG
SER 4
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB OG CA
1 2 HG OG CB CA
THR 5
1 1 H N -C CA
1 5 HA CA N C CB
1 5 HB CB CA OG1 CG2
1 2 HG1 OG1 CB CA
3 4 HG2 CG2 CB CA
TRP 9
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
1 1 HD1 CD1 NE1 CG
1 1 HE1 NE1 CD1 CE2
1 1 HE3 CE3 CD2 CZ3
1 1 HZ3 CZ3 CE3 CH2
1 1 HH2 CH2 CZ3 CZ2
1 1 HZ2 CZ2 CE2 CH2
TYR 8
1 1 H N -C CA
1 5 HA CA N C CB
2 6 HB CB CG CA
1 1 HD1 CD1 CG CE1
1 1 HD2 CD2 CG CE2
1 1 HE1 CE1 CD1 CZ
1 1 HE2 CE2 CD2 CZ
1 2 HH OH CZ CE1
VAL 5
1 1 H N -C CA
1 5 HA CA N C CB
1 5 HB CB CA CG1 CG2
3 4 HG1 CG1 CB CA
3 4 HG2 CG2 CB CA
DMSO 2
3 4 HD1 CD1 SD OD
3 4 HD2 CD2 SD OD
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